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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.strategy.cache.name;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;
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import eu.etaxonomy.cdm.strategy.cache.TagEnum;
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import eu.etaxonomy.cdm.strategy.cache.TaggedCacheHelper;
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import eu.etaxonomy.cdm.strategy.cache.TaggedText;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImplRegExBase;
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/**
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName>
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* interface.<BR>
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* The method implements a cache strategy for botanical names so no method has to be overwritten by
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* a subclass for botanic names.
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* Where differing from this default botanic name strategy other subclasses should overwrite the
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* existing methods, e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor
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* @author a.mueller
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*/
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public class NonViralNameDefaultCacheStrategy<T extends NonViralName<?>>
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extends NameCacheStrategyBase<T>
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implements INonViralNameCacheStrategy<T> {
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private static final Logger logger = Logger.getLogger(NonViralNameDefaultCacheStrategy.class);
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private static final long serialVersionUID = -6577757501563212669L;
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final static UUID uuid = UUID.fromString("1cdda0d1-d5bc-480f-bf08-40a510a2f223");
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protected String NameAuthorSeperator = " ";
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protected String BasionymStart = "(";
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protected String BasionymEnd = ")";
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protected String ExAuthorSeperator = " ex ";
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protected CharSequence BasionymAuthorCombinationAuthorSeperator = " ";
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@Override
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public UUID getUuid(){
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return uuid;
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}
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/**
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* Factory method
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy
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*/
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public static NonViralNameDefaultCacheStrategy NewInstance(){
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return new NonViralNameDefaultCacheStrategy();
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}
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/**
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* Factory method
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy
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*/
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public static <T extends NonViralName<?>> NonViralNameDefaultCacheStrategy<T> NewInstance(Class<T> clazz){
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return new NonViralNameDefaultCacheStrategy<T>();
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}
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/**
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* Constructor
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*/
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protected NonViralNameDefaultCacheStrategy(){
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super();
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}
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/* **************** GETTER / SETTER **************************************/
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/**
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* String that separates the NameCache part from the AuthorCache part
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* @return
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*/
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public String getNameAuthorSeperator() {
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return NameAuthorSeperator;
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}
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public void setNameAuthorSeperator(String nameAuthorSeperator) {
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NameAuthorSeperator = nameAuthorSeperator;
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}
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/**
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* String the basionym author part starts with e.g. '('.
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* This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymEnd() basionymEnd} attribute
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* @return
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*/
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public String getBasionymStart() {
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return BasionymStart;
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}
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public void setBasionymStart(String basionymStart) {
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BasionymStart = basionymStart;
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}
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/**
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* String the basionym author part ends with e.g. ')'.
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* This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymStart() basionymStart} attribute
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* @return
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*/
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public String getBasionymEnd() {
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return BasionymEnd;
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}
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public void setBasionymEnd(String basionymEnd) {
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BasionymEnd = basionymEnd;
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}
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/**
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* String to separate ex author from author.
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* @return
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*/
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public String getExAuthorSeperator() {
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return ExAuthorSeperator;
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}
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public void setExAuthorSeperator(String exAuthorSeperator) {
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ExAuthorSeperator = exAuthorSeperator;
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}
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/**
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* String that separates the basionym/original_combination author part from the combination author part
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* @return
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*/
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public CharSequence getBasionymAuthorCombinationAuthorSeperator() {
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return BasionymAuthorCombinationAuthorSeperator;
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}
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public void setBasionymAuthorCombinationAuthorSeperator( CharSequence basionymAuthorCombinationAuthorSeperator) {
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BasionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator;
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}
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//** *****************************************************************************************/
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@Override
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public String getTitleCache(T nonViralName) {
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return getTitleCache(nonViralName, null);
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}
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@Override
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public String getTitleCache(T nonViralName, HTMLTagRules htmlTagRules) {
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List<TaggedText> tags = getTaggedTitle(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags, htmlTagRules);
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return result;
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}
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}
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@Override
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public String getFullTitleCache(T nonViralName, HTMLTagRules htmlTagRules) {
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List<TaggedText> tags = getTaggedFullTitle(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags, htmlTagRules);
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return result;
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}
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}
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@Override
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public String getFullTitleCache(T nonViralName) {
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return getFullTitleCache(nonViralName, null);
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}
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/**
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* Generates and returns the "name cache" (only scientific name without author teams and year).
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* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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@Override
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public String getNameCache(T nonViralName) {
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List<TaggedText> tags = getTaggedName(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags);
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return result;
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}
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}
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// ******************* Authorship ******************************/
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@Override
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public String getAuthorshipCache(T nonViralName) {
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if (nonViralName == null){
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return null;
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}
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//cache protected
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if (nonViralName.isProtectedAuthorshipCache() == true) {
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return nonViralName.getAuthorshipCache();
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}
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return getNonCacheAuthorshipCache(nonViralName);
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}
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/**
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* Returns the authorshipcache string for the atomized authorship fields. Does not use the authorship field.
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* @throws NullPointerException if nonViralName is null.
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* @param nonViralName
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* @return
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*/
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protected String getNonCacheAuthorshipCache(T nonViralName){
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String result = "";
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INomenclaturalAuthor combinationAuthor = nonViralName.getCombinationAuthorship();
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INomenclaturalAuthor exCombinationAuthor = nonViralName.getExCombinationAuthorship();
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INomenclaturalAuthor basionymAuthor = nonViralName.getBasionymAuthorship();
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INomenclaturalAuthor exBasionymAuthor = nonViralName.getExBasionymAuthorship();
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String basionymPart = "";
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String authorPart = "";
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//basionym
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if (basionymAuthor != null || exBasionymAuthor != null){
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basionymPart = BasionymStart + getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor) + BasionymEnd;
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}
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if (combinationAuthor != null || exCombinationAuthor != null){
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authorPart = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
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}
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result = CdmUtils.concat(BasionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
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// if ("".equals(result)){
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// result = null;
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// }
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return result;
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}
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/**
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* Returns the AuthorCache part for a combination of an author and an ex author. This applies on combination authors
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* as well as on basionym/orginal combination authors.
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* @param author the author
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* @param exAuthor the ex-author
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* @return
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*/
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protected String getAuthorAndExAuthor(INomenclaturalAuthor author, INomenclaturalAuthor exAuthor){
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String result = "";
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String authorString = "";
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String exAuthorString = "";
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if (author != null){
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authorString = CdmUtils.Nz(author.getNomenclaturalTitle());
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}
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if (exAuthor != null){
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exAuthorString = CdmUtils.Nz(exAuthor.getNomenclaturalTitle());
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}
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if (exAuthorString.length() > 0 ){
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exAuthorString = exAuthorString + ExAuthorSeperator;
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}
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result = exAuthorString + authorString;
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return result;
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}
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/**
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* Checks if the given name should include the author in it's cached version.<BR>
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* This is usually the case but not for <i>species aggregates</i>.
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* @param nonViralName
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* @return
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*/
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protected boolean nameIncludesAuthorship(NonViralName<?> nonViralName){
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Rank rank = nonViralName.getRank();
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if (rank != null && rank.isSpeciesAggregate()){
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return false;
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}else{
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return true;
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}
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}
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// ************* TAGGED NAME ***************************************/
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@Override
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public List<TaggedText> getTaggedFullTitle(T nonViralName) {
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List<TaggedText> tags = new ArrayList<TaggedText>();
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//null
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if (nonViralName == null){
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return null;
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}
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//protected full title cache
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if (nonViralName.isProtectedFullTitleCache()){
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tags.add(new TaggedText(TagEnum.fullName, nonViralName.getFullTitleCache()));
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return tags;
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}
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//title cache
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// String titleCache = nonViralName.getTitleCache();
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List<TaggedText> titleTags = getTaggedTitle(nonViralName);
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tags.addAll(titleTags);
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//reference
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String microReference = nonViralName.getNomenclaturalMicroReference();
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INomenclaturalReference ref = nonViralName.getNomenclaturalReference();
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String referenceCache = null;
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if (ref != null){
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Reference reference = HibernateProxyHelper.deproxy(ref, Reference.class);
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//FIXME #5833 not needed anymore
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reference.setCacheStrategy(reference.getType().getCacheStrategy());
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referenceCache = reference.getNomenclaturalCitation(microReference);
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}
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//add to tags
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if (StringUtils.isNotBlank(referenceCache)){
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if (! referenceCache.trim().startsWith("in ")){
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String refConcat = ", ";
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tags.add(new TaggedText(TagEnum.separator, refConcat));
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}
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tags.add(new TaggedText(TagEnum.reference, referenceCache));
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}
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//nomenclatural status
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tags.addAll(getNomStatusTags(nonViralName, true, false));
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return tags;
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}
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/**
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* @param nonViralName
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* @param tags
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* @return
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*/
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@Override
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public List<TaggedText> getNomStatusTags(T nonViralName, boolean includeSeparatorBefore,
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boolean includeSeparatorAfter) {
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Set<NomenclaturalStatus> ncStati = nonViralName.getStatus();
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Iterator<NomenclaturalStatus> iterator = ncStati.iterator();
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List<TaggedText> nomStatusTags = new ArrayList<TaggedText>();
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while (iterator.hasNext()) {
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NomenclaturalStatus ncStatus = iterator.next();
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// since the NewInstance method of nomencatural status allows null as parameter
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// we have to check for null values here
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String nomStatusStr = "not defined";
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if(ncStatus.getType() != null){
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NomenclaturalStatusType statusType = ncStatus.getType();
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Language lang = Language.LATIN();
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Representation repr = statusType.getRepresentation(lang);
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if (repr != null){
|
|
381
|
nomStatusStr = repr.getAbbreviatedLabel();
|
|
382
|
}else{
|
|
383
|
String message = "No latin representation available for nom. status. " + statusType.getTitleCache();
|
|
384
|
logger.warn(message);
|
|
385
|
throw new IllegalStateException(message);
|
|
386
|
}
|
|
387
|
}else if(StringUtils.isNotBlank(ncStatus.getRuleConsidered())){
|
|
388
|
nomStatusStr = ncStatus.getRuleConsidered();
|
|
389
|
}
|
|
390
|
String statusSeparator = ", ";
|
|
391
|
if (includeSeparatorBefore){
|
|
392
|
nomStatusTags.add(new TaggedText(TagEnum.separator, statusSeparator));
|
|
393
|
}
|
|
394
|
nomStatusTags.add(new TaggedText(TagEnum.nomStatus, nomStatusStr));
|
|
395
|
if (includeSeparatorAfter){
|
|
396
|
nomStatusTags.add(new TaggedText(TagEnum.postSeparator, ","));
|
|
397
|
}
|
|
398
|
}
|
|
399
|
return nomStatusTags;
|
|
400
|
}
|
|
401
|
|
|
402
|
@Override
|
|
403
|
public List<TaggedText> getTaggedTitle(T nonViralName) {
|
|
404
|
if (nonViralName == null){
|
|
405
|
return null;
|
|
406
|
}
|
|
407
|
|
|
408
|
List<TaggedText> tags = new ArrayList<TaggedText>();
|
|
409
|
|
|
410
|
//TODO how to handle protected fullTitleCache here?
|
|
411
|
|
|
412
|
if (nonViralName.isProtectedTitleCache()){
|
|
413
|
//protected title cache
|
|
414
|
tags.add(new TaggedText(TagEnum.name, nonViralName.getTitleCache()));
|
|
415
|
return tags;
|
|
416
|
}else if (nonViralName.isHybridFormula()){
|
|
417
|
//hybrid formula
|
|
418
|
String hybridSeparator = NonViralNameParserImplRegExBase.hybridSign;
|
|
419
|
boolean isFirst = true;
|
|
420
|
List<HybridRelationship> rels = nonViralName.getOrderedChildRelationships();
|
|
421
|
for (HybridRelationship rel: rels){
|
|
422
|
if (! isFirst){
|
|
423
|
tags.add(new TaggedText(TagEnum.hybridSign, hybridSeparator));
|
|
424
|
}
|
|
425
|
isFirst = false;
|
|
426
|
tags.addAll(getTaggedTitle((T)rel.getParentName()));
|
|
427
|
}
|
|
428
|
return tags;
|
|
429
|
}else if (nonViralName.isAutonym()){
|
|
430
|
//Autonym
|
|
431
|
tags.addAll(handleTaggedAutonym(nonViralName));
|
|
432
|
}else{ //not Autonym
|
|
433
|
// String nameCache = nonViralName.getNameCache(); //OLD: CdmUtils.Nz(getNameCache(nonViralName));
|
|
434
|
List<TaggedText> nameTags = getTaggedName(nonViralName);
|
|
435
|
tags.addAll(nameTags);
|
|
436
|
String authorCache = getAuthorshipCache(nonViralName);
|
|
437
|
if (StringUtils.isNotBlank(authorCache)){
|
|
438
|
tags.add(new TaggedText(TagEnum.authors, authorCache));
|
|
439
|
}
|
|
440
|
}
|
|
441
|
return tags;
|
|
442
|
}
|
|
443
|
|
|
444
|
/**
|
|
445
|
* Returns the tag list of the name part (without author and reference).
|
|
446
|
* @param nonViralName
|
|
447
|
* @return
|
|
448
|
*/
|
|
449
|
@Override
|
|
450
|
public List<TaggedText> getTaggedName(T nonViralName) {
|
|
451
|
if (nonViralName == null){
|
|
452
|
return null;
|
|
453
|
}
|
|
454
|
List<TaggedText> tags = new ArrayList<TaggedText>();
|
|
455
|
Rank rank = nonViralName.getRank();
|
|
456
|
|
|
457
|
if (nonViralName.isProtectedNameCache()){
|
|
458
|
tags.add(new TaggedText(TagEnum.name, nonViralName.getNameCache()));
|
|
459
|
}else if (rank == null){
|
|
460
|
tags = getRanklessTaggedNameCache(nonViralName);
|
|
461
|
// }else if (nonViralName.isInfragenericUnranked()){
|
|
462
|
// result = getUnrankedInfragenericNameCache(nonViralName);
|
|
463
|
}else if (rank.isInfraSpecific()){
|
|
464
|
tags = getInfraSpeciesTaggedNameCache(nonViralName);
|
|
465
|
}else if (rank.isSpecies() || isAggregateWithAuthorship(nonViralName, rank) ){ //exception see #4288
|
|
466
|
tags = getSpeciesTaggedNameCache(nonViralName);
|
|
467
|
}else if (rank.isInfraGeneric()){
|
|
468
|
tags = getInfraGenusTaggedNameCache(nonViralName);
|
|
469
|
}else if (rank.isGenus()){
|
|
470
|
tags = getGenusOrUninomialTaggedNameCache(nonViralName);
|
|
471
|
}else if (rank.isSupraGeneric()){
|
|
472
|
tags = getGenusOrUninomialTaggedNameCache(nonViralName);
|
|
473
|
}else{
|
|
474
|
logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() + ") not yet implemented");
|
|
475
|
}
|
|
476
|
//TODO handle appended phrase here instead of different places, check first if this is true for all
|
|
477
|
//cases
|
|
478
|
|
|
479
|
return tags;
|
|
480
|
|
|
481
|
}
|
|
482
|
|
|
483
|
|
|
484
|
|
|
485
|
|
|
486
|
//***************************** PRIVATES ***************************************/
|
|
487
|
|
|
488
|
|
|
489
|
private boolean isAggregateWithAuthorship(T nonViralName, Rank rank) {
|
|
490
|
if (rank == null){
|
|
491
|
return false;
|
|
492
|
}else{
|
|
493
|
return rank.isSpeciesAggregate() && ( isNotBlank(nonViralName.getAuthorshipCache()) || nonViralName.getNomenclaturalReference() != null );
|
|
494
|
}
|
|
495
|
}
|
|
496
|
|
|
497
|
|
|
498
|
/**
|
|
499
|
* Returns the tag list for an autonym taxon.
|
|
500
|
*
|
|
501
|
* @see NonViralName#isAutonym()
|
|
502
|
* @see BotanicalName#isAutonym()
|
|
503
|
* @param nonViralName
|
|
504
|
* @return
|
|
505
|
*/
|
|
506
|
private List<TaggedText> handleTaggedAutonym(T nonViralName) {
|
|
507
|
List<TaggedText> tags = null;
|
|
508
|
if (nonViralName.isInfraSpecific()){
|
|
509
|
//species part
|
|
510
|
tags = getSpeciesTaggedNameCache(nonViralName);
|
|
511
|
|
|
512
|
//author
|
|
513
|
String authorCache = getAuthorshipCache(nonViralName);
|
|
514
|
if (StringUtils.isNotBlank(authorCache)){
|
|
515
|
tags.add(new TaggedText(TagEnum.authors, authorCache));
|
|
516
|
}
|
|
517
|
|
|
518
|
|
|
519
|
//infra species marker
|
|
520
|
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
|
|
521
|
//TODO handle exception
|
|
522
|
logger.warn("Rank for autonym does not exist or is not lower than species !!");
|
|
523
|
}else{
|
|
524
|
String infraSpeciesMarker = nonViralName.getRank().getAbbreviation();
|
|
525
|
if (StringUtils.isNotBlank(infraSpeciesMarker)){
|
|
526
|
tags.add(new TaggedText(TagEnum.rank, infraSpeciesMarker));
|
|
527
|
}
|
|
528
|
}
|
|
529
|
|
|
530
|
//infra species
|
|
531
|
String infraSpeciesPart = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim();
|
|
532
|
if (StringUtils.isNotBlank(infraSpeciesPart)){
|
|
533
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesPart));
|
|
534
|
}
|
|
535
|
|
|
536
|
} else if (nonViralName.isInfraGeneric()){
|
|
537
|
//genus part
|
|
538
|
tags =getGenusOrUninomialTaggedNameCache(nonViralName);
|
|
539
|
|
|
540
|
|
|
541
|
//infra species marker
|
|
542
|
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraGeneric()){
|
|
543
|
//TODO handle exception
|
|
544
|
logger.warn("Rank for autonym does not exist or is not lower than species !!");
|
|
545
|
}else{
|
|
546
|
Rank rank = nonViralName.getRank();
|
|
547
|
String infraGenericMarker = rank.getAbbreviation();
|
|
548
|
if (rank.equals(Rank.SECTION_BOTANY()) || rank.equals(Rank.SUBSECTION_BOTANY())){
|
|
549
|
infraGenericMarker = infraGenericMarker.replace("(bot.)", "");
|
|
550
|
}
|
|
551
|
if (StringUtils.isNotBlank(infraGenericMarker)){
|
|
552
|
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker));
|
|
553
|
}
|
|
554
|
}
|
|
555
|
|
|
556
|
//infra species
|
|
557
|
String infraGenericPart = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim();
|
|
558
|
if (StringUtils.isNotBlank(infraGenericPart)){
|
|
559
|
tags.add(new TaggedText(TagEnum.name, infraGenericPart));
|
|
560
|
}
|
|
561
|
|
|
562
|
}
|
|
563
|
|
|
564
|
return tags;
|
|
565
|
}
|
|
566
|
|
|
567
|
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Returns the tag list for rankless taxa.
|
|
571
|
* @param nonViralName
|
|
572
|
* @return
|
|
573
|
*/
|
|
574
|
protected List<TaggedText> getRanklessTaggedNameCache(NonViralName<?> nonViralName){
|
|
575
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
576
|
String speciesEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim();
|
|
577
|
if (StringUtils.isNotBlank(speciesEpi)){
|
|
578
|
tags.add(new TaggedText(TagEnum.name, speciesEpi));
|
|
579
|
}
|
|
580
|
|
|
581
|
String infraSpeciesEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet());
|
|
582
|
if (StringUtils.isNotBlank(infraSpeciesEpi)){
|
|
583
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesEpi));
|
|
584
|
}
|
|
585
|
|
|
586
|
//result += " (rankless)";
|
|
587
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
588
|
return tags;
|
|
589
|
}
|
|
590
|
|
|
591
|
/**
|
|
592
|
* Returns the tag list for the first epithet (including a hybrid sign if required).
|
|
593
|
* @param nonViralName
|
|
594
|
* @return
|
|
595
|
*/
|
|
596
|
private List<TaggedText> getUninomialTaggedPart(NonViralName<?> nonViralName) {
|
|
597
|
List<TaggedText> tags = new ArrayList<TaggedText>();
|
|
598
|
|
|
599
|
if (nonViralName.isMonomHybrid()){
|
|
600
|
addHybridPrefix(tags);
|
|
601
|
}
|
|
602
|
|
|
603
|
String uninomial = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim();
|
|
604
|
if (StringUtils.isNotBlank(uninomial)){
|
|
605
|
tags.add(new TaggedText(TagEnum.name, uninomial));
|
|
606
|
}
|
|
607
|
|
|
608
|
return tags;
|
|
609
|
}
|
|
610
|
|
|
611
|
/**
|
|
612
|
* Returns the tag list for an genus or higher taxon.
|
|
613
|
*
|
|
614
|
* @param nonViralName
|
|
615
|
* @return
|
|
616
|
*/
|
|
617
|
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(NonViralName<?> nonViralName){
|
|
618
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
619
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
620
|
return tags;
|
|
621
|
}
|
|
622
|
|
|
623
|
/**
|
|
624
|
* Returns the tag list for an infrageneric taxon (including species aggregates).
|
|
625
|
*
|
|
626
|
* @see #getSpeciesAggregateTaggedCache(NonViralName)
|
|
627
|
* @param nonViralName
|
|
628
|
* @return
|
|
629
|
*/
|
|
630
|
protected List<TaggedText> getInfraGenusTaggedNameCache(NonViralName<?> nonViralName){
|
|
631
|
Rank rank = nonViralName.getRank();
|
|
632
|
if (rank != null && rank.isSpeciesAggregate() && isBlank(nonViralName.getAuthorshipCache())){
|
|
633
|
return getSpeciesAggregateTaggedCache(nonViralName);
|
|
634
|
}
|
|
635
|
|
|
636
|
//genus
|
|
637
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
638
|
|
|
639
|
//marker
|
|
640
|
String infraGenericMarker;
|
|
641
|
if (rank != null){
|
|
642
|
try {
|
|
643
|
infraGenericMarker = rank.getInfraGenericMarker();
|
|
644
|
if (rank.equals(Rank.SECTION_BOTANY()) || rank.equals(Rank.SUBSECTION_BOTANY())){
|
|
645
|
infraGenericMarker = infraGenericMarker.replace("(bot.)", "");
|
|
646
|
}
|
|
647
|
} catch (UnknownCdmTypeException e) {
|
|
648
|
infraGenericMarker = "'unhandled infrageneric rank'";
|
|
649
|
}
|
|
650
|
}else{
|
|
651
|
infraGenericMarker = "'undefined infrageneric rank'";
|
|
652
|
}
|
|
653
|
String infraGenEpi = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim();
|
|
654
|
|
|
655
|
addInfraGenericPart(nonViralName, tags, infraGenericMarker, infraGenEpi);
|
|
656
|
|
|
657
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
658
|
return tags;
|
|
659
|
}
|
|
660
|
|
|
661
|
|
|
662
|
/**
|
|
663
|
* Default implementation for the infrageneric part of a name.
|
|
664
|
* This is usually the infrageneric marker and the infrageneric epitheton. But may be implemented differently e.g. for zoological
|
|
665
|
* names the infrageneric epitheton may be surrounded by brackets and the marker left out.
|
|
666
|
* @param nonViralName
|
|
667
|
* @param tags
|
|
668
|
* @param infraGenericMarker
|
|
669
|
*/
|
|
670
|
protected void addInfraGenericPart(NonViralName<?> name, List<TaggedText> tags, String infraGenericMarker, String infraGenEpi) {
|
|
671
|
//add marker
|
|
672
|
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker));
|
|
673
|
|
|
674
|
//add epitheton
|
|
675
|
if (StringUtils.isNotBlank(infraGenEpi)){
|
|
676
|
tags.add(new TaggedText(TagEnum.name, infraGenEpi));
|
|
677
|
}
|
|
678
|
}
|
|
679
|
|
|
680
|
/**
|
|
681
|
* Returns the tag list for a species aggregate (or similar) taxon.<BR>
|
|
682
|
* Possible ranks for a <i>species aggregate</i> are "aggr.", "species group", ...
|
|
683
|
* @param nonViralName
|
|
684
|
* @return
|
|
685
|
*/
|
|
686
|
protected List<TaggedText> getSpeciesAggregateTaggedCache(NonViralName<?> nonViralName){
|
|
687
|
if (! isBlank(nonViralName.getAuthorshipCache())){
|
|
688
|
List<TaggedText> result = getSpeciesTaggedNameCache(nonViralName);
|
|
689
|
return result;
|
|
690
|
}
|
|
691
|
|
|
692
|
|
|
693
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
694
|
|
|
695
|
addSpeciesAggregateTaggedEpithet(tags, nonViralName);
|
|
696
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
697
|
return tags;
|
|
698
|
}
|
|
699
|
|
|
700
|
/**
|
|
701
|
* Adds the aggregate tag to the tag list.
|
|
702
|
* @param tags
|
|
703
|
* @param nonViralName
|
|
704
|
*/
|
|
705
|
private void addSpeciesAggregateTaggedEpithet(List<TaggedText> tags, NonViralName<?> nonViralName) {
|
|
706
|
String marker;
|
|
707
|
try {
|
|
708
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
|
709
|
} catch (UnknownCdmTypeException e) {
|
|
710
|
marker = "'unknown aggregat type'";
|
|
711
|
}
|
|
712
|
if (StringUtils.isNotBlank(marker)){
|
|
713
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
|
714
|
}
|
|
715
|
}
|
|
716
|
|
|
717
|
|
|
718
|
/**
|
|
719
|
* Returns the tag list for a species taxon.
|
|
720
|
* @param nonViralName
|
|
721
|
* @return
|
|
722
|
*/
|
|
723
|
protected List<TaggedText> getSpeciesTaggedNameCache(NonViralName<?> nonViralName){
|
|
724
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
725
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
726
|
return tags;
|
|
727
|
}
|
|
728
|
|
|
729
|
/**
|
|
730
|
* Creates the tag list for an infraspecific taxon. In include is true the result will contain
|
|
731
|
* @param nonViralName
|
|
732
|
* @return
|
|
733
|
*/
|
|
734
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(T nonViralName){
|
|
735
|
return getInfraSpeciesTaggedNameCache(nonViralName, true);
|
|
736
|
}
|
|
737
|
|
|
738
|
/**
|
|
739
|
* Creates the tag list for an infraspecific taxon. If include is true the result will contain
|
|
740
|
* the infraspecific marker (e.g. "var.")
|
|
741
|
* @param nonViralName
|
|
742
|
* @param includeMarker
|
|
743
|
* @return
|
|
744
|
*/
|
|
745
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName, boolean includeMarker){
|
|
746
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
|
747
|
if (includeMarker){
|
|
748
|
String marker = (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
|
|
749
|
if (StringUtils.isNotBlank(marker)){
|
|
750
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
|
751
|
}
|
|
752
|
}
|
|
753
|
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet());
|
|
754
|
if (nonViralName.isTrinomHybrid()){
|
|
755
|
addHybridPrefix(tags);
|
|
756
|
}
|
|
757
|
|
|
758
|
infrSpecEpi = infrSpecEpi.trim().replace("null", "");
|
|
759
|
if (StringUtils.isNotBlank(infrSpecEpi)){
|
|
760
|
tags.add(new TaggedText(TagEnum.name, infrSpecEpi));
|
|
761
|
}
|
|
762
|
|
|
763
|
addAppendedTaggedPhrase(tags, nonViralName);
|
|
764
|
return tags;
|
|
765
|
}
|
|
766
|
|
|
767
|
|
|
768
|
/**
|
|
769
|
* Adds a tag for the hybrid sign and an empty separator to avoid trailing whitespaces.
|
|
770
|
* @param tags
|
|
771
|
*/
|
|
772
|
private void addHybridPrefix(List<TaggedText> tags) {
|
|
773
|
tags.add(new TaggedText(TagEnum.hybridSign, NonViralNameParserImplRegExBase.hybridSign));
|
|
774
|
tags.add(new TaggedText(TagEnum.separator, "")); //no whitespace separator
|
|
775
|
}
|
|
776
|
|
|
777
|
/**
|
|
778
|
* Creates the tag list for the genus and species part.
|
|
779
|
* @param nonViralName
|
|
780
|
* @return
|
|
781
|
*/
|
|
782
|
private List<TaggedText> getGenusAndSpeciesTaggedPart(NonViralName<?> nonViralName) {
|
|
783
|
//Uninomial
|
|
784
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
|
785
|
|
|
786
|
//InfraGenericEpi
|
|
787
|
boolean hasInfraGenericEpi = StringUtils.isNotBlank(nonViralName.getInfraGenericEpithet());
|
|
788
|
if (hasInfraGenericEpi){
|
|
789
|
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim();
|
|
790
|
if (nonViralName.isBinomHybrid()){
|
|
791
|
// addHybridPrefix(tags); FIXME hybridSign should be tag, but then we need to handle "(" ")" differently.
|
|
792
|
infrGenEpi = NonViralNameParserImplRegExBase.hybridSign + infrGenEpi;
|
|
793
|
}
|
|
794
|
infrGenEpi = "(" + infrGenEpi + ")";
|
|
795
|
tags.add(new TaggedText(TagEnum.name, infrGenEpi));
|
|
796
|
}
|
|
797
|
|
|
798
|
//Species Epi
|
|
799
|
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim();
|
|
800
|
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() ||
|
|
801
|
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){
|
|
802
|
addHybridPrefix(tags);
|
|
803
|
}
|
|
804
|
if (StringUtils.isNotBlank(specEpi)){
|
|
805
|
tags.add(new TaggedText(TagEnum.name, specEpi));
|
|
806
|
}
|
|
807
|
return tags;
|
|
808
|
}
|
|
809
|
|
|
810
|
/**
|
|
811
|
* Adds the tag for the appended phrase if an appended phrase exists
|
|
812
|
* @param tags
|
|
813
|
* @param nonViralName
|
|
814
|
*/
|
|
815
|
protected void addAppendedTaggedPhrase(List<TaggedText> tags, NonViralName<?> nonViralName){
|
|
816
|
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
|
|
817
|
String originalName = getOriginalNameString(nonViralName, tags);
|
|
818
|
if (StringUtils.isNotBlank(originalName)){
|
|
819
|
tags.add(new TaggedText(TagEnum.name, originalName));
|
|
820
|
}
|
|
821
|
if (StringUtils.isNotEmpty(appendedPhrase)){
|
|
822
|
tags.add(new TaggedText(TagEnum.name, appendedPhrase));
|
|
823
|
}
|
|
824
|
}
|
|
825
|
|
|
826
|
private String getOriginalNameString(NonViralName<?> currentName, List<TaggedText> originalNameTaggs) {
|
|
827
|
List<String> originalNameStrings = new ArrayList<String>(1);
|
|
828
|
for (NameRelationship nameRel : currentName.getRelationsToThisName()){ //handle list, just in case we have strange data; this may result in strange looking results
|
|
829
|
NameRelationshipType type = nameRel.getType();
|
|
830
|
if(type != null && type.equals(NameRelationshipType.ORIGINAL_SPELLING())){
|
|
831
|
String originalNameString;
|
|
832
|
TaxonNameBase<?,?> originalName = nameRel.getFromName();
|
|
833
|
if (!originalName.isInstanceOf(NonViralName.class)){
|
|
834
|
originalNameString = originalName.getTitleCache();
|
|
835
|
}else{
|
|
836
|
NonViralName<?> originalNvName = CdmBase.deproxy(originalName, NonViralName.class);
|
|
837
|
originalNameString = makeOriginalNameString(currentName, originalNvName, originalNameTaggs);
|
|
838
|
}
|
|
839
|
originalNameStrings.add("'" + originalNameString +"'");
|
|
840
|
}
|
|
841
|
}
|
|
842
|
if (originalNameStrings.size() > 0){
|
|
843
|
String result = CdmUtils.concat("", originalNameStrings.toArray(new String[originalNameStrings.size()])) ;
|
|
844
|
return result;
|
|
845
|
}else{
|
|
846
|
return null;
|
|
847
|
}
|
|
848
|
}
|
|
849
|
|
|
850
|
|
|
851
|
private String makeOriginalNameString(NonViralName<?> currentName, NonViralName<?> originalName, List<TaggedText> currentNameTags) {
|
|
852
|
//use cache if necessary
|
|
853
|
String cacheToUse = null;
|
|
854
|
if (originalName.isProtectedNameCache() && StringUtils.isNotBlank(originalName.getNameCache())){
|
|
855
|
cacheToUse = originalName.getNameCache();
|
|
856
|
}else if (originalName.isProtectedTitleCache() && StringUtils.isNotBlank(originalName.getTitleCache())){
|
|
857
|
cacheToUse = originalName.getTitleCache();
|
|
858
|
}else if (originalName.isProtectedFullTitleCache() && StringUtils.isNotBlank(originalName.getFullTitleCache())){
|
|
859
|
cacheToUse = originalName.getFullTitleCache();
|
|
860
|
}
|
|
861
|
if (cacheToUse != null){
|
|
862
|
return cacheToUse;
|
|
863
|
}
|
|
864
|
//use atomized data
|
|
865
|
//get originalNameParts array
|
|
866
|
String originalNameString = originalName.getNameCache();
|
|
867
|
if (originalNameString == null){
|
|
868
|
originalNameString = originalName.getTitleCache();
|
|
869
|
}
|
|
870
|
if (originalNameString == null){ //should not happen
|
|
871
|
originalNameString = originalName.getFullTitleCache();
|
|
872
|
}
|
|
873
|
String[] originalNameSplit = originalNameString.split("\\s+");
|
|
874
|
|
|
875
|
//get current name parts
|
|
876
|
String currentNameString = createString(currentNameTags);
|
|
877
|
String[] currentNameSplit = currentNameString.split("\\s+");
|
|
878
|
|
|
879
|
//compute string
|
|
880
|
String result = originalNameString;
|
|
881
|
for (int i = 0; i < Math.min(originalNameSplit.length, currentNameSplit.length); i++){
|
|
882
|
if (originalNameSplit[i].equals(currentNameSplit[i])){
|
|
883
|
result = result.replaceFirst(originalNameSplit[i], "").trim();
|
|
884
|
}
|
|
885
|
}
|
|
886
|
//old
|
|
887
|
// if (originalName.getGenusOrUninomial() != null && originalName.getGenusOrUninomial().equals(currentName.getGenusOrUninomial())){
|
|
888
|
//
|
|
889
|
// }
|
|
890
|
return result;
|
|
891
|
}
|
|
892
|
|
|
893
|
|
|
894
|
@Override
|
|
895
|
public String getLastEpithet(T taxonNameBase) {
|
|
896
|
Rank rank = taxonNameBase.getRank();
|
|
897
|
if(rank.isGenus() || rank.isSupraGeneric()) {
|
|
898
|
return taxonNameBase.getGenusOrUninomial();
|
|
899
|
} else if(rank.isInfraGeneric()) {
|
|
900
|
return taxonNameBase.getInfraGenericEpithet();
|
|
901
|
} else if(rank.isSpecies()) {
|
|
902
|
return taxonNameBase.getSpecificEpithet();
|
|
903
|
} else {
|
|
904
|
return taxonNameBase.getInfraSpecificEpithet();
|
|
905
|
}
|
|
906
|
}
|
|
907
|
|
|
908
|
|
|
909
|
/**
|
|
910
|
* @param tags
|
|
911
|
* @return
|
|
912
|
*/
|
|
913
|
private String createString(List<TaggedText> tags) {
|
|
914
|
return TaggedCacheHelper.createString(tags);
|
|
915
|
}
|
|
916
|
|
|
917
|
/**
|
|
918
|
* @param tags
|
|
919
|
* @param htmlTagRules
|
|
920
|
* @return
|
|
921
|
*/
|
|
922
|
private String createString(List<TaggedText> tags, HTMLTagRules htmlTagRules) {
|
|
923
|
return TaggedCacheHelper.createString(tags, htmlTagRules);
|
|
924
|
}
|
|
925
|
|
|
926
|
|
|
927
|
|
|
928
|
}
|